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The use of museum samples for large-scale sequence capture: a study of congeneric horseshoe bats (family Rhinolophidae)

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Museums hold most of the world’s most valuable biological specimens and tissues collected, including type
material that is often decades or even centuries old. Unfortunately, traditional museum collection and storage
methods were not designed to preserve the nucleic acids held within the material, often reducing its potential
viability and value for many genetic applications. High-throughput sequencing technologies and associated
applications offer new opportunities for obtaining sequence data from museum samples. In particular, target
sequence capture offers a promising approach for recovering large numbers of orthologous loci from relatively
small amounts of starting material. In the present study, we test the utility of target sequence capture for
obtaining data from museum-held material from a speciose mammalian genus: the horseshoe bats
(Rhinolophidae: Chiroptera). We designed a ‘bait’ for capturing > 3600 genes and applied this to 10 species of
horseshoe bat that had been collected between 93 and 7 years ago and preserved using a range of methods. We
found that the mean recovery rate per species was approximately 89% of target genes with partial sequence
coverage, ranging from 3024 to 3186 genes recovered. On average, we recovered 1206 genes with ≥ 90% sequence
coverage, per species. Our findings provide good support for the application of large-scale bait capture across
congeneric species spanning approximately 15 Myr of evolution. On the other hand, we observed no clear
association between the success of capture and the phylogenetic distance from the bait model, although sample
sizes precluded a formal test.

ADDITIONAL KEYWORDS: DNA – high-throughput sequencing – phylogenomics – pull-down – Rhinolophus – systematics – target enrichment.

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Ketersediaan

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Informasi Detail

Judul Seri

Biological Journal of the Linnean Society

No. Panggil

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Penerbit

: Graduate School of Economics, Waseda University., 2016

Deskripsi Fisik

Biological Journal of the Linnean Society, 2016, 117, 58–70

Bahasa

English

ISBN/ISSN

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Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

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